[English] 日本語
Yorodumi
- PDB-3shv: Crystal structure of human MCPH1 tandem BRCT domains-gamma H2AX c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3shv
TitleCrystal structure of human MCPH1 tandem BRCT domains-gamma H2AX complex
Components
  • Histone H2A.x
  • Microcephalin
KeywordsCELL CYCLE / tandem brct domains H2AX
Function / homology
Function and homology information


regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / chromatin-protein adaptor activity / XY body / protein localization to site of double-strand break / protein localization to centrosome / response to ionizing radiation / establishment of mitotic spindle orientation / site of DNA damage ...regulation of chromosome condensation / neuronal stem cell population maintenance / regulation of centrosome cycle / chromatin-protein adaptor activity / XY body / protein localization to site of double-strand break / protein localization to centrosome / response to ionizing radiation / establishment of mitotic spindle orientation / site of DNA damage / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / male germ cell nucleus / DNA methylation / positive regulation of DNA repair / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / DNA damage checkpoint signaling / SIRT1 negatively regulates rRNA expression / condensed nuclear chromosome / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / replication fork / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / bone development / cerebral cortex development / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / cellular senescence / nucleosome / heterochromatin formation / double-strand break repair / nucleosome assembly / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of inflammatory response / Oxidative Stress Induced Senescence / spermatogenesis / Estrogen-dependent gene expression / histone binding / damaged DNA binding / nuclear speck / Amyloid fiber formation / protein heterodimerization activity / centrosome / DNA damage response / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / BRCT domain / BRCT domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...Microcephalin-like / Microcephalin, mammal / Microcephalin protein / twin BRCT domain / BRCT domain / BRCT domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H2AX / Microcephalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsShao, Z.H. / Li, F.D. / Yan, W.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Specific recognition of phosphorylated tail of H2AX by the tandem BRCT domains of MCPH1 revealed by complex structure
Authors: Shao, Z.H. / Li, F.D. / Sy, S.M.-H. / Yan, W. / Zhang, Z. / Gong, D. / Wen, B. / Huen, M.S.Y. / Gong, Q. / Wu, J. / Shi, Y.
History
DepositionJun 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microcephalin
B: Microcephalin
C: Histone H2A.x
D: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)48,2164
Polymers48,2164
Non-polymers00
Water3,279182
1
A: Microcephalin
C: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)24,1082
Polymers24,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-7 kcal/mol
Surface area10220 Å2
MethodPISA
2
B: Microcephalin
D: Histone H2A.x


Theoretical massNumber of molelcules
Total (without water)24,1082
Polymers24,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.772, 132.860, 31.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Microcephalin


Mass: 22872.615 Da / Num. of mol.: 2 / Fragment: residues 639-835
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCPH1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEM0
#2: Protein/peptide Histone H2A.x


Mass: 1235.236 Da / Num. of mol.: 2 / Fragment: residues in UNP 134-143 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE IS FROM GENBANK NP_078872.2 MICROCEPHALIN ISOFORM 1. MICROCEPHALIN HAS A NATURAL ...THIS SEQUENCE IS FROM GENBANK NP_078872.2 MICROCEPHALIN ISOFORM 1. MICROCEPHALIN HAS A NATURAL VARIATIONS AT RESIDUE 761 POSITION IN UNIPROT DATABASE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Sodium acetate trihydrate, 100mM TRIS hydrochloride(pH 8.5), 30%(w/v) PEG4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2010
RadiationMonochromator: plane grating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 31233 / Num. obs: 31077 / % possible obs: 99.5 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 / Χ2: 0.85 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.144.30.3514440.704197.8
2.14-2.184.70.33115170.762199.5
2.18-2.224.90.30915430.7181100
2.22-2.2650.27315320.821197.5
2.26-2.315.40.22714820.7621100
2.31-2.375.40.19415250.7741100
2.37-2.425.40.17415760.772199
2.42-2.495.60.16315000.793199.7
2.49-2.565.50.14615320.791100
2.56-2.655.50.11615520.83199.2
2.65-2.745.60.10515310.9041100
2.74-2.855.50.08815720.9091100
2.85-2.985.50.07115280.927199.7
2.98-3.145.40.05815951.0551100
3.14-3.335.50.05315401.067199.9
3.33-3.595.40.0515810.9511100
3.59-3.955.30.05215920.927199.7
3.95-4.525.10.04815920.774199.3
4.52-5.75.20.04215970.774199.6
5.7-504.80.03217460.882199

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.53 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.08 Å
Translation2.5 Å45.08 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SHT

3sht


Resolution: 2.1→45.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2394 / WRfactor Rwork: 0.1959 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8437 / SU B: 4.066 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1851 / SU Rfree: 0.1709 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1564 5 %RANDOM
Rwork0.1966 ---
obs0.1988 31018 99.5 %-
all-31233 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.65 Å2 / Biso mean: 33.1432 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 0 182 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223112
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.974245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1715386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75723.621116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38515.058513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0371514
X-RAY DIFFRACTIONr_chiral_restr0.0970.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222308
X-RAY DIFFRACTIONr_mcbond_it0.9171.51954
X-RAY DIFFRACTIONr_mcangle_it1.73923176
X-RAY DIFFRACTIONr_scbond_it2.5631158
X-RAY DIFFRACTIONr_scangle_it4.1454.51069
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 115 -
Rwork0.207 2062 -
all-2177 -
obs--98.33 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more